# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 05:49:54 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-[(4~{Z})-2-[(1~{S})-1-azanyl-3-methyl-butyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)C1=N\C(=C/c2ccc(O)cc2)C(=O)N1CC(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 VYA  VYA  '2-[(4~{Z})-2-[(1~{S})-1-azanyl-3-methyl-butyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic acid'  L-peptide  45  24  .  2022-09-22  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VYA
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 VYA  C2   C  CR16  0  -0.314   4.5065  -1.1839  -0.8559
 VYA  C4   C  CR16  0  -0.377   5.7035   0.6829   0.0929
 VYA  C5   C  CR16  0  -0.282   4.4984   1.2599   0.4435
 VYA  C6   C  CR16  0  -0.299   3.3094  -0.5993  -0.5015
 VYA  C3   C  CH3   0  -0.649  -3.4644  -4.0961   1.6077
 VYA  C10  C  CH3   0  -0.667  -4.5570  -2.7936  -0.2371
 VYA  C20  C  CH2   0  -0.422  -2.2781  -2.1194   0.6494
 VYA  C16  C  CH1   0  -0.232  -1.9128  -1.2493  -0.5708
 VYA  N    N  NH2   0  -0.780  -1.2906  -1.9531  -1.6731
 VYA  C14  C  CR5   0   0.583  -0.9947  -0.1611  -0.1114
 VYA  N15  N  N     0  -0.481   0.2861  -0.2170  -0.2002
 VYA  N13  N  NR5   0  -0.563  -1.4557   0.9677   0.5403
 VYA  C17  C  CH2   0  -0.471  -2.8095   1.4138   0.6524
 VYA  C    C  C     0   0.548  -3.2932   2.0496  -0.6351
 VYA  O19  O  O     0  -0.424  -2.6200   2.1593  -1.6247
 VYA  C12  C  CR5   0   0.536  -0.3635   1.7528   0.8622
 VYA  O25  O  O     0  -0.445  -0.4065   2.8415   1.3966
 VYA  C9   C  CR5   0   0.087   0.7763   0.9396   0.3940
 VYA  C7   C  CR6   0   0.132   3.2746   0.6415   0.1566
 VYA  C1   C  CR6   0   0.361   5.7160  -0.5474  -0.5628
 VYA  O3   O  OH1   0  -0.617   6.8493  -1.1628  -0.9274
 VYA  OXT  O  OH1   0  -0.582  -4.5445   2.4564  -0.5185
 VYA  H1   H  HCR6  0   0.270   4.5165  -2.1400  -1.3644
 VYA  H2   H  HCR6  0   0.279   6.6336   1.1878   0.3266
 VYA  H3   H  HCR6  0   0.265   4.5053   2.2162   0.9529
 VYA  H4   H  HCR6  0   0.278   2.3837  -1.1059  -0.7341
 VYA  H5   H  H     0   0.268   2.2026   2.2703   1.0538
 VYA  H6   H  HCH3  0   0.229  -4.0995  -4.9590   1.4025
 VYA  H7   H  HCH3  0   0.227  -2.5259  -4.4651   2.0244
 VYA  H8   H  HCH3  0   0.216  -3.9580  -3.4961   2.3758
 VYA  H9   H  HCH1  0   0.217  -2.7498  -3.9331  -0.3912
 VYA  H10  H  HCH3  0   0.230  -4.4428  -2.3151  -1.2112
 VYA  H11  H  HCH3  0   0.235  -5.2473  -3.6276  -0.3745
 VYA  H12  H  HCH3  0   0.218  -5.0376  -2.0762   0.4333
 VYA  H13  H  HCH2  0   0.226  -2.7292  -1.4979   1.4321
 VYA  H14  H  HCH2  0   0.244  -1.3491  -2.5154   1.0727
 VYA  H15  H  HCH1  0   0.257  -2.8272  -0.7883  -0.9570
 VYA  H16  H  HNH2  0   0.349  -0.4515  -2.4216  -1.3527
 VYA  H17  H  HNH2  0   0.359  -1.9136  -2.6776  -2.0058
 VYA  H19  H  HCH2  0   0.313  -3.4723   0.5937   0.9340
 VYA  H20  H  HCH2  0   0.331  -2.8776   2.1435   1.4618
 VYA  H21  H  HOH1  0   0.480   7.6177  -0.6327  -0.6859
 VYA  H22  H  HOH1  0   0.491  -4.8517   2.8565  -1.3465
 VYA  C8   C  C1    0  -0.382   2.0610   1.3174   0.5528
 VYA  C21  C  CH1   0  -0.244  -3.2306  -3.2767   0.3423

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 VYA  N    C16  single    1.448  0.020  1.448
 VYA  C17  N13  single    1.430  0.020  1.430
 VYA  C17  C    single    1.515  0.020  1.515
 VYA  O19  C    double    1.202  0.020  1.202
 VYA  O25  C12  double    1.214  0.020  1.214
 VYA  N13  C12  single    1.383  0.020  1.383
 VYA  N13  C14  single    1.383  0.020  1.383
 VYA  C16  C14  single    1.496  0.020  1.496
 VYA  C16  C20  single    1.543  0.020  1.543
 VYA  C12  C9   single    1.476  0.020  1.476
 VYA  C14  N15  double    1.285  0.020  1.285
 VYA  C21  C10  single    1.526  0.020  1.526
 VYA  C21  C20  single    1.530  0.020  1.530
 VYA  C21  C3   single    1.526  0.020  1.526
 VYA  N15  C9   single    1.390  0.020  1.390
 VYA  C9   C8   double    1.349  0.020  1.349
 VYA  C8   C7   single    1.444  0.020  1.444
 VYA  C6   C7   aromatic  1.405  0.020  1.405
 VYA  C6   C2   aromatic  1.378  0.020  1.378
 VYA  C7   C5   aromatic  1.401  0.020  1.401
 VYA  C2   C1   aromatic  1.398  0.020  1.398
 VYA  C5   C4   aromatic  1.381  0.020  1.381
 VYA  C1   C4   aromatic  1.394  0.020  1.394
 VYA  C1   O3   single    1.340  0.020  1.340
 VYA  C    OXT  single    1.321  0.020  1.321
 VYA  C2   H1   single    0.930  0.020  1.080
 VYA  C4   H2   single    0.930  0.020  1.080
 VYA  C5   H3   single    0.930  0.020  1.080
 VYA  C6   H4   single    0.930  0.020  1.080
 VYA  C8   H5   single    0.930  0.020  1.080
 VYA  C3   H6   single    0.970  0.020  1.090
 VYA  C3   H7   single    0.970  0.020  1.090
 VYA  C3   H8   single    0.970  0.020  1.090
 VYA  C21  H9   single    0.970  0.020  1.090
 VYA  C10  H10  single    0.970  0.020  1.090
 VYA  C10  H11  single    0.970  0.020  1.090
 VYA  C10  H12  single    0.970  0.020  1.090
 VYA  C20  H13  single    0.970  0.020  1.090
 VYA  C20  H14  single    0.970  0.020  1.090
 VYA  C16  H15  single    0.970  0.020  1.090
 VYA  N    H16  single    0.890  0.020  1.040
 VYA  N    H17  single    0.890  0.020  1.040
 VYA  C17  H19  single    0.970  0.020  1.090
 VYA  C17  H20  single    0.970  0.020  1.090
 VYA  O3   H21  single    0.850  0.020  0.980
 VYA  OXT  H22  single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 VYA  H1   C2   C1   119.50  3.000
 VYA  H1   C2   C6   120.21  3.000
 VYA  C1   C2   C6   120.29  3.000
 VYA  H2   C4   C1   120.32  3.000
 VYA  H2   C4   C5   119.96  3.000
 VYA  C1   C4   C5   119.72  3.000
 VYA  H3   C5   C7   119.44  3.000
 VYA  H3   C5   C4   118.84  3.000
 VYA  C7   C5   C4   121.72  3.000
 VYA  H4   C6   C7   119.58  3.000
 VYA  H4   C6   C2   119.32  3.000
 VYA  C7   C6   C2   121.10  3.000
 VYA  H8   C3   H7   107.80  3.000
 VYA  H8   C3   H6   107.67  3.000
 VYA  H7   C3   H6   107.76  3.000
 VYA  H8   C3   C21  110.94  3.000
 VYA  H7   C3   C21  111.51  3.000
 VYA  H6   C3   C21  110.98  3.000
 VYA  H12  C10  H11  107.50  3.000
 VYA  H12  C10  H10  107.80  3.000
 VYA  H11  C10  H10  106.79  3.000
 VYA  H12  C10  C21  110.92  3.000
 VYA  H11  C10  C21  110.84  3.000
 VYA  H10  C10  C21  112.75  3.000
 VYA  H14  C20  H13  106.15  3.000
 VYA  H14  C20  C16  107.99  3.000
 VYA  H13  C20  C16  110.02  3.000
 VYA  H14  C20  C21  109.41  3.000
 VYA  H13  C20  C21  108.41  3.000
 VYA  C16  C20  C21  114.53  3.000
 VYA  H15  C16  C14  108.34  3.000
 VYA  H15  C16  N    107.17  3.000
 VYA  C14  C16  N    108.87  3.000
 VYA  H15  C16  C20  108.60  3.000
 VYA  C14  C16  C20  108.22  3.000
 VYA  N    C16  C20  115.45  3.000
 VYA  H17  N    H16  106.43  3.000
 VYA  H17  N    C16  109.49  3.000
 VYA  H16  N    C16  109.87  3.000
 VYA  N13  C14  N15  113.60  3.000
 VYA  N15  C14  C16  123.97  3.000
 VYA  N13  C14  C16  122.27  3.000
 VYA  C9   N15  C14  106.61  3.000
 VYA  C12  N13  C17  123.53  3.000
 VYA  C12  N13  C14  108.05  3.000
 VYA  C17  N13  C14  127.40  3.000
 VYA  H20  C17  H19  105.84  3.000
 VYA  H20  C17  C    109.24  3.000
 VYA  H19  C17  C    109.92  3.000
 VYA  H20  C17  N13  109.01  3.000
 VYA  H19  C17  N13  111.15  3.000
 VYA  C    C17  N13  111.51  3.000
 VYA  OXT  C    O19  125.11  3.000
 VYA  OXT  C    C17  110.90  3.000
 VYA  O19  C    C17  123.99  3.000
 VYA  C9   C12  O25  131.38  3.000
 VYA  C9   C12  N13  102.90  3.000
 VYA  O25  C12  N13  125.72  3.000
 VYA  C12  C9   N15  108.76  3.000
 VYA  N15  C9   C8   128.29  3.000
 VYA  C12  C9   C8   122.95  3.000
 VYA  C8   C7   C6   124.24  3.000
 VYA  C6   C7   C5   117.65  3.000
 VYA  C8   C7   C5   118.11  3.000
 VYA  O3   C1   C4   122.73  3.000
 VYA  O3   C1   C2   117.75  3.000
 VYA  C4   C1   C2   119.52  3.000
 VYA  H21  O3   C1   110.69  3.000
 VYA  H22  OXT  C    110.60  3.000
 VYA  H5   C8   C7   115.32  3.000
 VYA  H5   C8   C9   115.11  3.000
 VYA  C7   C8   C9   129.57  3.000
 VYA  H9   C21  C20  108.32  3.000
 VYA  H9   C21  C10  108.48  3.000
 VYA  C20  C21  C10  112.21  3.000
 VYA  H9   C21  C3   107.51  3.000
 VYA  C20  C21  C3   109.58  3.000
 VYA  C10  C21  C3   110.60  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 VYA  CONST_01  C5   C7   C6   C2      0.00   0.0  0
 VYA  CONST_02  C5   C4   C1   C2      0.00   0.0  0
 VYA  CONST_03  C6   C7   C5   C4      0.00   0.0  0
 VYA  CONST_04  C6   C2   C1   C4      0.00   0.0  0
 VYA  CONST_05  C1   C2   C6   C7      0.00   0.0  0
 VYA  CONST_06  C1   C4   C5   C7      0.00   0.0  0
 VYA  CONST_07  C9   C12  N13  C14     0.00   0.0  0
 VYA  CONST_08  C12  C9   N15  C14     0.00   0.0  0
 VYA  CONST_09  C12  N13  C14  N15     0.00   0.0  0
 VYA  CONST_10  N13  C12  C9   N15     0.00   0.0  0
 VYA  CONST_11  C9   N15  C14  N13     0.00   0.0  0
 VYA  CONST_12  C8   C7   C6   C2    180.00   0.0  0
 VYA  CONST_13  C8   C7   C5   C4    180.00   0.0  0
 VYA  CONST_14  O3   C1   C4   C5    180.00   0.0  0
 VYA  CONST_15  O3   C1   C2   C6    180.00   0.0  0
 VYA  CONST_16  C12  N13  C14  C16   180.00   0.0  0
 VYA  CONST_17  C9   N15  C14  C16   180.00   0.0  0
 VYA  CONST_18  O25  C12  N13  C14   180.00   0.0  0
 VYA  CONST_19  C17  N13  C14  N15   180.00   0.0  0
 VYA  CONST_20  C9   C12  N13  C17   180.00   0.0  0
 VYA  CONST_21  H2   C4   C1   C2    180.00   0.0  0
 VYA  CONST_22  H1   C2   C1   C4    180.00   0.0  0
 VYA  CONST_23  H4   C6   C7   C5    180.00   0.0  0
 VYA  CONST_24  H3   C5   C7   C6    180.00   0.0  0
 VYA  CONST_25  C17  N13  C14  C16     0.00   0.0  0
 VYA  CONST_26  O25  C12  N13  C17     0.00   0.0  0
 VYA  CONST_27  H22  OXT  C    C17   180.00   0.0  0
 VYA  Var_01    C9   C8   C7   C5    179.96  30.0  3
 VYA  Var_02    C7   C8   C9   N15     0.08  30.0  2
 VYA  Var_03    C    C17  N13  C14   -76.37  30.0  1
 VYA  Var_04    O19  C    C17  N13     0.18  30.0  3
 VYA  Var_05    C16  C20  C21  C3    177.44  30.0  3
 VYA  Var_06    H10  C10  C21  C3   -172.53  30.0  3
 VYA  Var_07    H6   C3   C21  C10    58.78  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 VYA  chir_01  C16  N  C14  C20  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 VYA  plan-1  C16  0.020
 VYA  plan-1  C14  0.020
 VYA  plan-1  N15  0.020
 VYA  plan-1  N13  0.020
 VYA  plan-1  C17  0.020
 VYA  plan-1  C12  0.020
 VYA  plan-1  O25  0.020
 VYA  plan-1  C9   0.020
 VYA  plan-1  C8   0.020
 VYA  plan-2  C2   0.020
 VYA  plan-2  C4   0.020
 VYA  plan-2  C5   0.020
 VYA  plan-2  C6   0.020
 VYA  plan-2  C7   0.020
 VYA  plan-2  C1   0.020
 VYA  plan-2  O3   0.020
 VYA  plan-2  H1   0.020
 VYA  plan-2  H2   0.020
 VYA  plan-2  H3   0.020
 VYA  plan-2  H4   0.020
 VYA  plan-2  C8   0.020
 VYA  plan-3  C17  0.020
 VYA  plan-3  C    0.020
 VYA  plan-3  O19  0.020
 VYA  plan-3  OXT  0.020
 VYA  plan-3  H22  0.020

